Skip to main content
Article thumbnail
Location of Repository

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

By Amy J Powell, Gavin C Conant, Douglas E Brown, Ignazio Carbone and Ralph A Dean
Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2330156
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Citations

    1. (2005). A human-curated annotation of the Candida albicans genome. PLOS Genetics
    2. (2006). A: Fungal tyrosinases: new prospects in molecular characteristics, bioengineering and biotechnological applications.
    3. (2002). A: GenomeHistory: a software tool and its application to fully sequenced genomes.
    4. (2006). A: The dawn of fungal pathogen genomics. Annual Review of Phytopathology
    5. (2002). Aravind L: The role of lineagespecific gene family expansion in the evolution of Eukaryotes. Genome Research
    6. Aspergillus oryzae genome
    7. (2005). BG: Functional Analysis of All Nonribosomal Peptide Synthetases
    8. (2005). Birren B: Genomics of the fungal kingdom: Insights into eukaryotic biology. Genome Research
    9. (2003). BS: Extensive gene gain associated with adaptive evolution of poxviruses.
    10. (2007). BW: Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus . Molecular Ecology
    11. (2007). Calvo AM: Elucidation of veA- dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics. Applied Microbiology and Biotechnology
    12. (2001). Carniel E: Ecological fitness, genomic islands and bacterial pathogenicity – A Darwinian view of the evolution of microbes. EMBO reports
    13. CD: From Genes to Genomes: A New Paradigm for Studying Fungal Pathogenesis in Magnaporthe oryzae .
    14. (2006). CM: Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi . Molecular Ecology
    15. (2005). Common themes in the genome strategies of pathogens.
    16. (2006). Comparative genomics and genome evolution in yeasts.
    17. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing.
    18. (2006). DB: Evidence of RIP (repeatinduced point mutation) in transposase sequences of Aspergillus oryzae . Fungal Genetics and Biology
    19. (1996). DB: Trihydroxynaphthalene Reductase from Magnaporthe grisea: Realization of an Active Center Inhibitor and Elucidation of the Kinetic Mechanism. Biochemistry
    20. (1997). DC: Molecular evidence for an ancient duplication of the entire yeast genome. Nature
    21. (2000). Diversity of homology-dependent gene silencing strategies in fungi. Current Opinion in Microbiology
    22. (2000). DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae . Nature
    23. (2007). Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum .
    24. Entrez Genome [http://www.ncbi.nlm.nih.gov/sites/ent rez?db=genome]
    25. (2004). et al.: Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance.
    26. (2005). Experimental evolution of conflict mediation between genomes. PNAS
    27. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli .
    28. (1996). FC: Mutualistic Fungal Endophytes Express a Proteinase that Is Homologous to Proteases Suspected to Be Important in Fungal Pathogenicity. Plant Physiology
    29. (1994). FC: Purification and characterization of an endophytic fungal proteinase that is abundantly expressed in the infected host grass. Plant Physiology
    30. (2001). Force A: The probability of preservation of a newly arisen gene duplicate. Genetics
    31. Fungal Genome Initiative [http://www.broad.mit.edu/annota tion/fungi/fgi/]
    32. (2005). G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea . Genome Biology
    33. (2006). G: A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
    34. (2003). GB: Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascyomycetes. PNAS
    35. (2006). Gene duplication event in family 12 glycosyl hydrolase from Phytophthora spp. Fungal Genetics and Biology
    36. (2007). Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster.
    37. (2007). Genome sequence analysis of the cellulolytic fungus Trichoderma reesei (syn. Hypocrea jecorina) reveals a surprisingly limited inventory of carbohydrate active enzymes.
    38. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology
    39. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. Nature
    40. (2005). Genome sequencing and analysis of Aspergillus oryzae . Nature
    41. (2008). GenomeBMC Genomics
    42. (2006). Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus . Nature
    43. (2006). Goldman WE: Defining virulence genes in the dimorphic fungi. Annu Rev Microbiol
    44. (1979). Graph Theory: An introductory Course.
    45. (2007). Gurr SJ: Magnaporthe grisea Cutinase2 Mediates Appressorium Differentiation and Host Penetration and Is Required for Full Virulence. The Plant Cell
    46. (2006). Howlett BJ: Parallels in fungal pathogenesis on plant and animal hosts. Eukaryotic Cell
    47. (2004). Hughes BD: A model explaining the size distribution of gene and protein families. Mathematical Biosciences
    48. (2006). Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis . Nature
    49. (2007). JJ: Transcriptional adaptation of Mycosphaerella graminicola to programmed cell death (PCD) of its susceptible host. Molecular Plant-Microbe Interactions
    50. (2005). JW: Fungal secondary metabolism-from biochemistry to genomics. Nature Reviews: Microbiology
    51. (2007). Kamoun S: Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic Oomycetes . The Plant Cell
    52. (2002). Karev GP: The structure of the protein universe and genome evolution. Nature
    53. (1992). Knowles PF: Galatose oxidase of Dactylium dendroides .
    54. (1996). Kover PX: The Red Queen hypothesis and plant/pathogen interactions. Annu Rev Phytopathol
    55. (2006). L: Genome comparison using Gene Ontology (GO) with statistical testing.
    56. (2005). Leong SA: Evolution of an avirulence gene AVR1-CO39, concomitant with the evolution and differentiation of Magnaporthe oryzae . Molecular Plant-Microbe Interactions
    57. (2003). Li WH: Molecular evolution meets the genomics revolution. Nature Genetics Supplement
    58. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
    59. (2002). Mayama S: Repeat-induced point mutation (RIP) in Magnaporthe grisea : Implications for its sexual cycle in the natural field context. Molecular Microbiology
    60. (2004). MV: The extracellular constitutive production of chitin deacetylase in Metarhizium anisopliae : possible edge to entomopathogenic fungi in the biological control of insect pests.
    61. (2002). Mycotoxin genetics and gene clusters.
    62. (2004). NP: LaeA, a regulator of secondary metabolism in Aspergillus species. Eukaryotic Cell
    63. (1993). Oellermann OR: Applied and Algorithmic Graph Theory.
    64. (2003). On the trail of a cereal killer: Exploring the Biology of Magnaporthe grisea . Annu Rev Microbiol
    65. (2006). Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science
    66. (2005). Poxvirus genome evolution by gene gain and loss. Molecular Phylogenetics and Evolution
    67. (2008). RA: GT-Miner: a graphtheoretic data miner, viewer and model processor. Personal communication
    68. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature
    69. (2005). Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum. Genetics
    70. (1997). Roberts DW: Adaptation of proteases and carbohydrases of saprophytic, phytopathogenic and entomopathogenic fungi to the requirements of their ecological niches.
    71. (1995). Rohlf FJ: Biometry Third edition. WH Freeman and Company,
    72. (2006). RP: Emergence of a new disease as a result of interspecific virulence gene transfer. Nature Genetics
    73. (2006). SA: Recent insights into R gene evolution. Molecular Plant Pathology
    74. scale-free networks and genome biology.
    75. (2004). Selker EU: RIP: the evolutionary cost of genome defense. Trends in Genetics
    76. (2005). Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature
    77. (2007). Talbot NJ: Generation of reactive oxygen species by fungal NADPH oxidases is required for the rice blast disease. PNAS
    78. (2006). Taylor JW: Dating divergences in the fungal tree of life: Review and new analyses. Mycologia
    79. (2001). Taylor JW: Fungal molecular evolution: Gene trees and geologic time. The Mycota VII Part B: Systematics and Evolution
    80. (2007). The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes.
    81. (1998). The frequency distribution of gene family sizes in complete genomes. Mol Bio Evol
    82. (2007). The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science
    83. (2004). The Gene OC: The Gene Ontology (GO) database and informatics resource.
    84. The Gene Ontology database
    85. (2005). The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans . Science
    86. (2004). The genome of the diatom Thalassiosira pseudonana : Ecology, evolution, and metabolism. Science
    87. (2003). The genome sequence of the filamentous fungus Neurospora crassa . Nature
    88. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea . Nature
    89. (2001). The phylogeny of plant and animal pathogens in the Ascomycota. Physiological and Molecular Plant Pathology
    90. (2004). Tudzynski P: Functional analysis of H2O2-generating systems in Botrytis cinerea : the major Cu-Zn-superoxide dismutase (BCSOD1) contributes to virulence on french bean, whereas a glucose oxidase (BCGOD1) is dispensable. Molecular Plant Pathology
    91. (1992). Vetterling WT: Numerical Recipes in C: the art of scientific computing. second edition.
    92. (2006). Whole genome comparison of Aspergillus flavus and A. oryzae. Medical Mycology
    93. (2007). Widespread lateral gene transfer from intracellular Bacteria to multicellular Eukaryotes. Science
    94. (2007). Wolfe KH: Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Molecular Systems Biology

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.